Religious institutions have been priced out of offering civil partnership ceremonies by high licensing fees, according to Unitarian ministers and liberal rabbis.

Councils are charging churches and synagogues up to 16 times more for a three-year licence to hold civil partnership ceremonies than for a permanent licence to conduct marriages, Guardian research has revealed.

Conor Marron, co-founder of the campaign group Coalition for Equal Marriage, said the gap in fees amounted to discrimination by councils. "This comes as yet another example of the differences between civil partnerships and marriages, which are not immediately apparent," he said.

For more than a decade permanent marriage licences for religious buildings have been issued at a standard national cost of £120, set by the registrar general. But while the Equality Act of 2010 made it legal for civil partnership ceremonies to take place in religious buildings after December 2011, it also allowed local councils to set their own fees and conditions.

Hotels and other commercial venues pay much more for short-term marriage licences than religious buildings do for permanent ones. In contrast, many councils have chosen to charge places of worship the same fee as commercial venues for a three-year civil partnership licence. Gloucestershire, Buckinghamshire and Surrey county councils charge £2,000 for a three-year licence to hold civil partnership ceremonies in religious buildings.

Unitarians, Quakers and liberal Jews are willing to offer civil partnership ceremonies, in contrast to the Church of England, Catholic church and Orthodox Jews.

The Rev Andrew Brown, of the Memorial church in Cambridge, said the £1,550 cost of a licence meant his congregation had also been unable to offer civil partnership ceremonies: "It's just a prohibitive price, so we didn't go ahead to offer civil partnerships. We haven't got that kind of money – we're a small congregation."

Rabbi Aaron Goldstein, of the Northwood and Pinner Liberal synagogue in Hillingdon, west London, said: "Our synagogue decided not to register itself because of having to pay. We would have reconsidered if there had been immediate demand, but it feels a bit like being penalised for something that should be a right in society." Hillingdon council charges £460 for a three-year licence.

Guardian research sampling 42 councils across the country found the median cost of a licence to hold civil partnerships in religious buildings was £1,000 for three years. Several councils said it would not be fair to charge religious organisations less than hotels.